5JJV

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.

Bebel, A.Karaca, E.Kumar, B.Stark, W.M.Barabas, O.

(2016) Elife 5

  • DOI: 10.7554/eLife.19706
  • Primary Citation of Related Structures:  
    5JJV, 5JK0

  • PubMed Abstract: 
  • Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA dif H , representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway ...

    Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA dif H , representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in dif H defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine recombinase XerHA, B363Helicobacter pylori 26695Mutation(s): 0 
Gene Names: xerHHP_0675
UniProt
Find proteins for O25386 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25386 
Go to UniProtKB:  O25386
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25386
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')C, E13Helicobacter pylori 26695
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')D, F17Helicobacter pylori 26695
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.38α = 90
b = 115.22β = 90
c = 235.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
PHENIXmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2018-09-19
    Changes: Advisory, Data collection, Database references